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- PDB-5lih: Structure of a peptide-substrate bound to PKCiota core kinase domain -

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Basic information

Entry
Database: PDB / ID: 5lih
TitleStructure of a peptide-substrate bound to PKCiota core kinase domain
Components
  • PKC Epsilon pseudo substrate sequence
  • Protein kinase C iota type
KeywordsTRANSFERASE / aPKC / Polarity / Complex
Function / homology
Function and homology information


ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / negative regulation of sodium ion transmembrane transport / positive regulation of mucus secretion / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Golgi vesicle budding / toxin catabolic process / PAR polarity complex / Tight junction interactions / DAG and IP3 signaling ...ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / negative regulation of sodium ion transmembrane transport / positive regulation of mucus secretion / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Golgi vesicle budding / toxin catabolic process / PAR polarity complex / Tight junction interactions / DAG and IP3 signaling / positive regulation of lipid catabolic process / protein kinase C / establishment of apical/basal cell polarity / diacylglycerol-dependent serine/threonine kinase activity / mucus secretion / Effects of PIP2 hydrolysis / negative regulation of glial cell apoptotic process / eye photoreceptor cell development / regulation of insulin secretion involved in cellular response to glucose stimulus / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / membrane organization / cellular response to chemical stress / intermediate filament cytoskeleton / regulation of release of sequestered calcium ion into cytosol / macrophage activation involved in immune response / cell-cell junction organization / positive regulation of cell-substrate adhesion / positive regulation of fibroblast migration / protein targeting to membrane / tight junction / insulin secretion / response to morphine / positive regulation of wound healing / positive regulation of Notch signaling pathway / positive regulation of cytokinesis / cell-substrate adhesion / synaptic transmission, GABAergic / establishment of cell polarity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / cell leading edge / cellular response to ethanol / locomotory exploration behavior / brush border / signaling receptor activator activity / positive regulation of epithelial cell migration / actin monomer binding / positive regulation of endothelial cell apoptotic process / positive regulation of glial cell proliferation / Role of phospholipids in phagocytosis / bicellular tight junction / xenobiotic catabolic process / regulation of postsynaptic membrane neurotransmitter receptor levels / intercellular bridge / positive regulation of superoxide anion generation / vesicle-mediated transport / 14-3-3 protein binding / negative regulation of protein ubiquitination / cytoskeleton organization / secretion / p75NTR recruits signalling complexes / SHC1 events in ERBB2 signaling / response to interleukin-1 / lipopolysaccharide-mediated signaling pathway / actin filament organization / positive regulation of synaptic transmission, GABAergic / cell periphery / positive regulation of D-glucose import / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / enzyme activator activity / establishment of localization in cell / positive regulation of NF-kappaB transcription factor activity / positive regulation of neuron projection development / positive regulation of insulin secretion / peptidyl-serine phosphorylation / phospholipid binding / Pre-NOTCH Transcription and Translation / Schaffer collateral - CA1 synapse / cellular response to insulin stimulus / KEAP1-NFE2L2 pathway / G alpha (z) signalling events / cell migration / cellular response to prostaglandin E stimulus / MAPK cascade / microtubule cytoskeleton / cellular response to hypoxia / negative regulation of neuron apoptotic process / protein phosphorylation / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / positive regulation of MAPK cascade / endosome / intracellular signal transduction / cilium / apical plasma membrane / Golgi membrane / cell division / protein serine kinase activity
Similarity search - Function
Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / Protein kinase C, delta/epsilon/eta/theta types / PB1 domain / PB1 domain / PB1 domain / : ...Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / Protein kinase C, delta/epsilon/eta/theta types / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / : / THIOCYANATE ION / Protein kinase C iota type / Protein kinase C epsilon type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsSoriano, E.V. / Purkiss, A.G. / McDonald, N.Q.
CitationJournal: Dev.Cell / Year: 2016
Title: aPKC Inhibition by Par3 CR3 Flanking Regions Controls Substrate Access and Underpins Apical-Junctional Polarization.
Authors: Soriano, E.V. / Ivanova, M.E. / Fletcher, G. / Riou, P. / Knowles, P.P. / Barnouin, K. / Purkiss, A. / Kostelecky, B. / Saiu, P. / Linch, M. / Elbediwy, A. / Kjr, S. / O'Reilly, N. / ...Authors: Soriano, E.V. / Ivanova, M.E. / Fletcher, G. / Riou, P. / Knowles, P.P. / Barnouin, K. / Purkiss, A. / Kostelecky, B. / Saiu, P. / Linch, M. / Elbediwy, A. / Kjr, S. / O'Reilly, N. / Snijders, A.P. / Parker, P.J. / Thompson, B.J. / McDonald, N.Q.
History
DepositionJul 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line ..._entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C iota type
B: Protein kinase C iota type
F: PKC Epsilon pseudo substrate sequence
G: PKC Epsilon pseudo substrate sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,37917
Polymers84,7984
Non-polymers1,58113
Water45025
1
A: Protein kinase C iota type
F: PKC Epsilon pseudo substrate sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2179
Polymers42,3992
Non-polymers8187
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-28 kcal/mol
Surface area14590 Å2
MethodPISA
2
B: Protein kinase C iota type
G: PKC Epsilon pseudo substrate sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1628
Polymers42,3992
Non-polymers7636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-29 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.980, 84.230, 111.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABFG

#1: Protein Protein kinase C iota type / Atypical protein kinase C-lambda/iota / aPKC-lambda/iota / nPKC-iota


Mass: 40333.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCI, DXS1179E / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P41743, protein kinase C
#2: Protein/peptide PKC Epsilon pseudo substrate sequence


Mass: 2065.476 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: UniProt: Q02156*PLUS

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Non-polymers , 5 types, 38 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32% Peg 2000 MME, 0.08 M KSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.25→67.28 Å / Num. obs: 12144 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 6.3
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a8w

3a8w


Resolution: 3.25→67.28 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.57
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 628 5.17 %Random Selection
Rwork0.2566 ---
obs0.258 12144 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.25→67.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 81 25 5293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035393
X-RAY DIFFRACTIONf_angle_d0.7337319
X-RAY DIFFRACTIONf_dihedral_angle_d16.2923156
X-RAY DIFFRACTIONf_chiral_restr0.048795
X-RAY DIFFRACTIONf_plane_restr0.008936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2501-3.57720.29921550.28462836X-RAY DIFFRACTION100
3.5772-4.09480.31891530.26142825X-RAY DIFFRACTION99
4.0948-5.15870.26671580.22912872X-RAY DIFFRACTION99
5.1587-67.2950.26261620.26472983X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5634-0.38650.83221.2484-0.44791.27920.1909-0.4599-0.21380.06770.0078-0.1507-0.09910.1084-0.08610.5457-0.0329-0.01760.24460.0332-0.009441.604316.375749.5889
21.461-1.23550.69612.0702-1.22743.0092-0.1065-0.07150.09990.14610.1867-0.239-0.4706-0.1104-0.07160.26170.00330.08660.0814-0.04270.22438.763726.879329.146
30.9691-0.83410.03340.93910.19951.6382-0.3994-0.3016-0.13140.33710.51330.5348-0.4243-0.9619-0.62420.35990.170.07390.63090.13870.267424.91122.722544.6708
43.6813-1.825-1.7071.84991.44061.15650.5553-0.113-0.1729-0.43670.0864-0.05740.17540.14660.87290.46660.0921-0.24110.15880.13780.327844.8658-0.053547.1979
51.8669-0.1594-0.76192.28830.65050.9681-0.1523-0.2829-0.4843-0.14720.4415-0.37560.30970.24990.26460.9088-0.2306-0.05110.30230.0930.127141.058126.9182105.0244
61.7224-0.01450.56524.0438-1.08453.25290.21790.05380.16350.3378-0.4720.1548-0.12430.29540.21040.4114-0.08920.05580.2199-0.02620.226838.533737.534184.6605
71.5103-2.069-0.042.86780.34422.8994-0.25820.0092-0.32150.79290.22740.84530.7979-1.0645-0.13530.5876-0.11160.0640.37990.01410.356924.528133.3322100.1572
83.44070.06690.13641.89351.59264.03650.5693-0.4503-0.16170.6217-0.0561-0.4913-0.08880.75520.74551.0815-0.4664-0.36490.40840.0810.539245.024310.3537103.0618
92.9466-1.10040.06162.5896-0.46411.974-0.42730.21060.28660.3636-0.0671-0.02670.40550.21070.16640.7365-0.0296-0.11460.2930.20940.431933.731512.822629.4297
102.902-2.93431.69183.7546-1.19233.10110.32310.04230.30950.7929-0.372-0.46740.77360.3583-0.03190.72620.1864-0.09170.4043-0.19240.239935.885224.274885.2518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 240:323)
2X-RAY DIFFRACTION2chain 'A' and (resseq 324:532)
3X-RAY DIFFRACTION3chain 'A' and (resseq 533:558)
4X-RAY DIFFRACTION4chain 'A' and (resseq 559:578)
5X-RAY DIFFRACTION5chain 'B' and (resseq 240:323)
6X-RAY DIFFRACTION6chain 'B' and (resseq 324:532)
7X-RAY DIFFRACTION7chain 'B' and (resseq 533:558)
8X-RAY DIFFRACTION8chain 'B' and (resseq 559:578)
9X-RAY DIFFRACTION9chain 'F'
10X-RAY DIFFRACTION10chain 'G'

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